Merge pull request #276 from nf-core/dev

Patch release 1.1.1

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js,cff}]
+[*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -45,6 +45,6 @@ body:
         * Nextflow version _(eg. 22.10.1)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/funcscan _(eg. 1.1, 1.5, 1.8.2)_

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/func
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/funcscan/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/funcscan _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/funcscan/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/funcscan _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/awsfulltest.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v1
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/awstest.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v1
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/funcscan'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/funcscan ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/funcscan ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/clean-up.yml

@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.8"
           architecture: "x64"
 
       - name: Install dependencies

.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier

CHANGELOG.md

@@ -3,7 +3,25 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.1.0 - British Beans on Toast - [2023-04-26]
+## v1.1.1 - [2023-05-24]
+
+### `Added`
+
+- [#270](https://github.com/nf-core/funcscan/pull/270) Merged pipeline template of nf-core/tools version 2.8 and updated modules accordingly. (by @jasmezz, @jfy133)
+- [#274](https://github.com/nf-core/funcscan/pull/274) Update all modules: changed docker links according to the change of quay.io as default repository and Pyrodigal annotation output now zipped. (by @jasmezz)
+- [#275](https://github.com/nf-core/funcscan/pull/275) Save DRAMP database in the common database directory if `--save_databases` is supplied. (by @jasmezz)
+
+### `Fixed`
+
+- [#272](https://github.com/nf-core/funcscan/pull/272) Fix typo in Prokka output path in modules.config. (by @jasmezz)
+- [#273](https://github.com/nf-core/funcscan/pull/273) Update Ampir module after input bugfix in module. (reported by @mathavanpu, fix by @louperelo)
+- [#276](https://github.com/nf-core/funcscan/pull/276) Fix Pyrodigal parameters in modules.config. (by @jasmezz)
+
+### `Dependencies`
+
+### `Deprecated`
+
+## v1.1.0 - British Beans on Toast - [2023-04-27]
 
 ### `Added`
 

README.md

@@ -7,7 +7,7 @@
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/funcscan)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23funcscan-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/funcscan)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23funcscan-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/funcscan)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -30,38 +30,54 @@ The nf-core/funcscan AWS full test dataset are contigs generated by the MGnify s
 
 ![funcscan metro workflow](docs/images/funcscan_metro_workflow.png)
 
-## Quick Start
+## Usage
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
+> **Note**
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
+> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
+> with `-profile test` before running the workflow on actual data.
 
-2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
+First, prepare a samplesheet with your input data that looks as follows:
 
-3. Download the pipeline and test it on a minimal dataset with a single command:
+`samplesheet.csv`:
 
-   ```bash
-   nextflow run nf-core/funcscan -profile test,YOURPROFILE --outdir <OUTDIR>
-   ```
+```csv
+sample,fasta
+CONTROL_REP1,AEG588A1_001.fasta
+CONTROL_REP2,AEG588A1_002.fasta
+CONTROL_REP3,AEG588A1_003.fasta
+```
 
-   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
+Each row represents a (multi-)fasta file of assembled contig sequences.
 
-   > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
-   > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-   > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
-   > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
+Now, you can run the pipeline using:
 
-4. Start running your own analysis!
+```bash
+nextflow run nf-core/funcscan \
+   -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
+   --input samplesheet.csv \
+   --outdir <OUTDIR> \
+   --run_amp_screening \
+   --run_arg_screening \
+   --run_bgc_screening
+```
 
-   ```bash
-   nextflow run nf-core/funcscan --input samplesheet.csv --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --run_amp_screening --run_arg_screening --run_bgc_screening
-   ```
+> **Warning:**
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
+> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
-## Documentation
+For more details, please refer to the [usage documentation](https://nf-co.re/funcscan/usage) and the [parameter documentation](https://nf-co.re/funcscan/parameters).
 
-The nf-core/funcscan pipeline comes with documentation about the pipeline [usage](https://nf-co.re/funcscan/usage), [parameters](https://nf-co.re/funcscan/parameters) and [output](https://nf-co.re/funcscan/output).
+## Pipeline output
+
+To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/funcscan/results) tab on the nf-core website pipeline page.
+For more details about the output files and reports, please refer to the
+[output documentation](https://nf-co.re/funcscan/output).
 
 ## Credits
 
-nf-core/funcscan was originally written by Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, and James A. Fellows Yates.
+nf-core/funcscan was originally written by Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 

conf/igenomes.config

@@ -36,6 +36,14 @@ params {
             macs_gsize  = "2.7e9"
             blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
         }
+        'CHM13' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
+            bwamem2     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
+            gff         = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
+            mito_name   = "chrM"
+        }
         'GRCm38' {
             fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
             bwa         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"

conf/modules.config

@@ -62,7 +62,7 @@ process {
 
     withName: PROKKA {
         publishDir = [
-            path: { "${params.outdir}/annotation/prokka/}" },
+            path: { "${params.outdir}/annotation/prokka/" },
             mode: params.publish_dir_mode,
             enabled: params.save_annotations,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
@@ -162,14 +162,14 @@ process {
             path: { "${params.outdir}/annotation/pyrodigal/${meta.id}" },
             mode: params.publish_dir_mode,
             enabled: params.save_annotations,
-            pattern: "*.{faa,fna}",
+            pattern: "*.{faa,fna,gff,score}.gz",
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
         ext.args = [
             params.annotation_pyrodigal_singlemode ? "-p single" : "-p meta",
-            params.annotation_prodigal_closed ? "-c" : "",
-            params.annotation_prodigal_forcenonsd ? "-n" : "",
-            "-g ${params.annotation_prodigal_transtable}"
+            params.annotation_pyrodigal_closed ? "-c" : "",
+            params.annotation_pyrodigal_forcenonsd ? "-n" : "",
+            "-g ${params.annotation_pyrodigal_transtable}"
         ].join(' ').trim()
     }
 
@@ -496,4 +496,13 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
+    withName: DRAMP_DOWNLOAD {
+        publishDir = [
+            path: { "${params.outdir}/databases/dramp" },
+            mode: params.publish_dir_mode,
+            enabled: params.save_databases,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 }

docs/output.md

@@ -10,7 +10,7 @@ The output of nf-core/funcscan provides reports for each of the functional group
 
 As a general workflow, we recommend to first look at the summary reports ([ARGs](#hamronization), [AMPs](#ampcombi), [BGCs](#combgc)), to get a general overview of what hits have been found across all the tools of each functional group. After which, you can explore the specific output directories of each tool to get more detailed information about each result. The tool-specific output directories also includes the output from the functional annotation steps of either [prokka](https://github.com/tseemann/prokka), [pyrodigal](https://github.com/althonos/pyrodigal), [prodigal](https://github.com/hyattpd/Prodigal), or [Bakta](https://github.com/oschwengers/bakta) if the `--save_annotations` flag was set.
 
-Similarly, all downloaded databases are saved (i.e. from [antiSMASH](https://docs.antismash.secondarymetabolites.org), [AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder), [Bakta](https://github.com/oschwengers/bakta), and/or [DeepARG](https://bitbucket.org/gusphdproj/deeparg-ss/src/master)) into the output directory `<outdir>/downloads/` if the `--save_databases` flag was set.
+Similarly, all downloaded databases are saved (i.e. from [antiSMASH](https://docs.antismash.secondarymetabolites.org), [AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder), [Bakta](https://github.com/oschwengers/bakta), [DeepARG](https://bitbucket.org/gusphdproj/deeparg-ss/src/master), and/or [AMPcombi](https://github.com/Darcy220606/AMPcombi)) into the output directory `<outdir>/downloads/` if the `--save_databases` flag was set.
 
 Furthermore, for reproducibility, versions of all software used in the run is presented in a [MultiQC](http://multiqc.info) report.